4-75407765-A-G

Variant names:

• chr4-75407765-A-G
• rs2903698
• ENST00000505930.2:n.159+26353T>C

Variant summary

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

The ENST00000505930.2(ENSG00000251185):​n.159+26353T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,200 control chromosomes in the GnomAD database, including 3,463 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 0.20 (3462 hom., cov: 32)
  • Exomes 𝑓: 0.28 (1 hom.)
• Consequence: ENSG00000251185 ENST00000505930.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998
• Publications: 9 publications found

Genes affected

ENSG00000251185 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505930.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251185	ENST00000505930.2	TSL:3	n.159+26353T>C		intron	N/A
	ENSG00000250735	ENST00000507739.5	TSL:3	n.98+6473A>G		intron	N/A
	ENSG00000251185	ENST00000510744.1	TSL:3	n.332+26353T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29795 AN: 152064 Hom.: 3456 Cov.: 32

Gnomad AFR AF: 0.0947

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.0943

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.175

GnomAD4 exome AF: 0.278 AC: 5 AN: 18 Hom.: 1 AF XY: 0.214 AC XY: 3 AN XY: 14

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.278 AC: 5 AN: 18

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.196 AC: 29826 AN: 152182 Hom.: 3462 Cov.: 32 AF XY: 0.199 AC XY: 14799 AN XY: 74408

African (AFR) AF: 0.0952 AC: 3957 AN: 41546

American (AMR) AF: 0.166 AC: 2543 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 596 AN: 3462

East Asian (EAS) AF: 0.0947 AC: 490 AN: 5176

South Asian (SAS) AF: 0.172 AC: 829 AN: 4826

European-Finnish (FIN) AF: 0.335 AC: 3547 AN: 10584

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17246 AN: 67984

Other (OTH) AF: 0.174 AC: 368 AN: 2110

Alfa AF: 0.231 Hom.: 18952

Bravo AF: 0.179

Asia WGS AF: 0.147 AC: 514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.24
DANN	Benign	0.87
PhyloP100		-1.0
Mutation Taster		=65/35	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2903698; hg19: chr4-76332975;