rs973796

Variant names:

• chr4-144502816-A-C
• rs973796
• ENST00000649263.1:n.328-86838T>G

Your query was ambiguous. Multiple possible variants found:

• chr4-144502816-A-C
• chr4-144502816-A-G

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-86838T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 152,110 control chromosomes in the GnomAD database, including 8,984 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 0.32 (8984 hom., cov: 33)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 7 publications found

Genes affected

ENSG00000285713 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649263.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285713	ENST00000649263.1		n.328-86838T>G		intron	N/A	ENSP00000497507.1	A0A3B3ISY7
	ENSG00000285783	ENST00000648340.1		n.138+6425T>G		intron	N/A
	ENSG00000285783	ENST00000650526.1		n.223-86838T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48347 AN: 151992 Hom.: 8975 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.318 AC: 48359 AN: 152110 Hom.: 8984 Cov.: 33 AF XY: 0.325 AC XY: 24160 AN XY: 74344

African (AFR) AF: 0.125 AC: 5201 AN: 41560

American (AMR) AF: 0.308 AC: 4705 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1132 AN: 3472

East Asian (EAS) AF: 0.309 AC: 1598 AN: 5166

South Asian (SAS) AF: 0.530 AC: 2552 AN: 4818

European-Finnish (FIN) AF: 0.500 AC: 5277 AN: 10560

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.394 AC: 26746 AN: 67954

Other (OTH) AF: 0.318 AC: 672 AN: 2114

Alfa AF: 0.354 Hom.: 1761

Bravo AF: 0.288

Asia WGS AF: 0.370 AC: 1285 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.8
DANN	Benign	0.60
PhyloP100		1.1

Splicing

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: rs973796;

hg19: chr4-145423968;