chr7-55017274-C-T

Variant names:

• chr7-55017274-C-T
• rs6965469
• ENST00000836965.1:n.1301C>T

Variant summary

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

The ENST00000836965.1(ENSG00000308870):​n.1301C>T 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 0.0403 in 152,246 control chromosomes in the GnomAD database, including 189 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 0.040 (189 hom., cov: 33)
• Consequence: ENSG00000308870 ENST00000836965.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489
• Publications: 10 publications found

Genes affected

ENSG00000308870 (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 (EAS) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000836965.1. 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
	ENSG00000308870	ENST00000836965.1		n.1301C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0403 AC: 6128 AN: 152132 Hom.: 188 Cov.: 33

Gnomad AFR AF: 0.0292

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0319

Gnomad ASJ AF: 0.0320

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.0570

Gnomad FIN AF: 0.0358

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0388

Gnomad OTH AF: 0.0397

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

GnomAD4 genome AF: 0.0403 AC: 6138 AN: 152246 Hom.: 189 Cov.: 33 AF XY: 0.0402 AC XY: 2995 AN XY: 74414

African (AFR) AF: 0.0293 AC: 1219 AN: 41574

American (AMR) AF: 0.0319 AC: 488 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0320 AC: 111 AN: 3468

East Asian (EAS) AF: 0.172 AC: 893 AN: 5178

South Asian (SAS) AF: 0.0562 AC: 271 AN: 4822

European-Finnish (FIN) AF: 0.0358 AC: 380 AN: 10602

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0388 AC: 2639 AN: 67986

Other (OTH) AF: 0.0426 AC: 90 AN: 2112

Alfa AF: 0.0378 Hom.: 110

Bravo AF: 0.0405

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.32
DANN	Benign	0.79
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs6965469; hg19: chr7-55084967;