rs3960787

Variant names:

• chr4-102995560-A-G
• rs3960787
• NM_139173.4:c.-1-3848T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_139173.4(SLC9B1):​c.-1-3848T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0903 in 152,214 control chromosomes in the GnomAD database, including 802 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.090 (802 hom., cov: 32)
• Consequence: SLC9B1 NM_139173.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89
• Publications: 4 publications found

Genes affected

SLC9B1 (HGNC:24244): (solute carrier family 9 member B1) The protein encoded by this gene is a sodium/hydrogen exchanger and transmembrane protein. Highly conserved orthologs of this gene have been found in other mammalian species. The expression of this gene may be limited to testis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_139173.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC9B1	NM_139173.4	MANE Select	c.-1-3848T>C		intron	N/A	NP_631912.3	Q4ZJI4-1
	SLC9B1	NM_001100874.3		c.-1-3848T>C		intron	N/A	NP_001094344.2	Q4ZJI4-3
	SLC9B1	NR_047513.2		n.108-3848T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC9B1	ENST00000296422.12	TSL:1 MANE Select	c.-1-3848T>C		intron	N/A	ENSP00000296422.7	Q4ZJI4-1
	SLC9B1	ENST00000394789.7	TSL:1	c.-1-3848T>C		intron	N/A	ENSP00000378269.3	Q4ZJI4-3
	SLC9B1	ENST00000504216.5	TSL:1	n.-1-3848T>C		intron	N/A	ENSP00000423072.1	D6RA80

Frequencies

GnomAD3 genomes AF: 0.0904 AC: 13745 AN: 152096 Hom.: 801 Cov.: 32

Gnomad AFR AF: 0.0314

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.0611

Gnomad SAS AF: 0.0867

Gnomad FIN AF: 0.0753

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.118

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0903 AC: 13744 AN: 152214 Hom.: 802 Cov.: 32 AF XY: 0.0904 AC XY: 6727 AN XY: 74432

African (AFR) AF: 0.0313 AC: 1301 AN: 41568

American (AMR) AF: 0.149 AC: 2279 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 454 AN: 3470

East Asian (EAS) AF: 0.0610 AC: 316 AN: 5180

South Asian (SAS) AF: 0.0870 AC: 419 AN: 4818

European-Finnish (FIN) AF: 0.0753 AC: 798 AN: 10600

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7670 AN: 67978

Other (OTH) AF: 0.117 AC: 247 AN: 2112

Alfa AF: 0.0971 Hom.: 711

Bravo AF: 0.0933

Asia WGS AF: 0.0720 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.3
DANN	Benign	0.79
PhyloP100		1.9
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3960787;

hg19: chr4-103916717;