rs7548917

Variant names:

• chr1-100773820-T-C
• rs7548917
• ENST00000762830.1:n.84+7855A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-100773820-T-C
• chr1-100773820-T-G

Variant summary

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

The ENST00000762830.1(ENSG00000299357):​n.84+7855A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 151,384 control chromosomes in the GnomAD database, including 18,659 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 0.49 (18659 hom., cov: 29)
• Consequence: ENSG00000299357 ENST00000762830.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.980
• Publications: 2 publications found

Genes affected

ENSG00000299357 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762830.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299357	ENST00000762830.1		n.84+7855A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74262 AN: 151268 Hom.: 18646 Cov.: 29

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.491 AC: 74315 AN: 151384 Hom.: 18659 Cov.: 29 AF XY: 0.494 AC XY: 36509 AN XY: 73924

African (AFR) AF: 0.561 AC: 23120 AN: 41218

American (AMR) AF: 0.529 AC: 8052 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1271 AN: 3466

East Asian (EAS) AF: 0.607 AC: 3112 AN: 5130

South Asian (SAS) AF: 0.499 AC: 2392 AN: 4796

European-Finnish (FIN) AF: 0.505 AC: 5261 AN: 10428

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29675 AN: 67834

Other (OTH) AF: 0.481 AC: 1010 AN: 2098

Alfa AF: 0.479 Hom.: 2945

Bravo AF: 0.497

Asia WGS AF: 0.552 AC: 1922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.72
DANN	Benign	0.16
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs7548917; hg19: chr1-101239376; COSMIC: COSV59978413;