3-195932298-A-G

Variant names:

• chr3-195932298-A-G
• rs4927680
• ENST00000607976.3:n.614+16944T>C

Variant summary

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

The NR_197445.1(LOC124906253):​n.1053+16944T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 152,000 control chromosomes in the GnomAD database, including 9,552 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 0.35 (9552 hom., cov: 32)
• Consequence: LOC124906253 NR_197445.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 6 publications found

Genes affected

ENSG00000290762 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_197445.1. 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
	LOC124906253	NR_197445.1		n.1053+16944T>C		intron	N/A
	LOC124906253	NR_197446.1		n.4125+15027T>C		intron	N/A
	LOC124906253	NR_197447.1		n.3725-3217T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290762	ENST00000607976.3	TSL:6	n.614+16944T>C		intron	N/A
	ENSG00000290762	ENST00000641484.1		n.1500-8088T>C		intron	N/A
	ENSG00000290762	ENST00000726774.1		n.351+15037T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53486 AN: 151882 Hom.: 9536 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.352 AC: 53535 AN: 152000 Hom.: 9552 Cov.: 32 AF XY: 0.352 AC XY: 26119 AN XY: 74296

African (AFR) AF: 0.317 AC: 13138 AN: 41462

American (AMR) AF: 0.379 AC: 5789 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1403 AN: 3468

East Asian (EAS) AF: 0.180 AC: 929 AN: 5154

South Asian (SAS) AF: 0.401 AC: 1928 AN: 4812

European-Finnish (FIN) AF: 0.384 AC: 4064 AN: 10576

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.368 AC: 24989 AN: 67944

Other (OTH) AF: 0.374 AC: 787 AN: 2104

Alfa AF: 0.365 Hom.: 1251

Bravo AF: 0.346

Asia WGS AF: 0.280 AC: 976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.36
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs4927680; hg19: chr3-195659169;