rs11977885

Variant names:

• chr7-4646888-A-G
• rs11977885
• ENST00000741934.1:n.713A>G

Variant summary

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

The ENST00000741934.1(ENSG00000286874):​n.713A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,054 control chromosomes in the GnomAD database, including 6,261 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 0.28 (6261 hom., cov: 32)
• Consequence: ENSG00000286874 ENST00000741934.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152
• Publications: 5 publications found

Genes affected

ENSG00000286874 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741934.1. 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
	ENSG00000286874	ENST00000741934.1		n.713A>G		non_coding_transcript_exon	Exon 5 of 5
	ENSG00000286874	ENST00000741935.1		n.786A>G		non_coding_transcript_exon	Exon 5 of 5
	ENSG00000286874	ENST00000741936.1		n.713A>G		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41949 AN: 151934 Hom.: 6230 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.276 AC: 42021 AN: 152054 Hom.: 6261 Cov.: 32 AF XY: 0.277 AC XY: 20574 AN XY: 74322

African (AFR) AF: 0.393 AC: 16296 AN: 41470

American (AMR) AF: 0.259 AC: 3964 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 499 AN: 3470

East Asian (EAS) AF: 0.294 AC: 1518 AN: 5162

South Asian (SAS) AF: 0.304 AC: 1466 AN: 4818

European-Finnish (FIN) AF: 0.255 AC: 2695 AN: 10560

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14661 AN: 67974

Other (OTH) AF: 0.247 AC: 520 AN: 2106

Alfa AF: 0.230 Hom.: 16191

Bravo AF: 0.279

Asia WGS AF: 0.314 AC: 1093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.5
DANN	Benign	0.53
PhyloP100		0.15
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11977885; hg19: chr7-4686519;