rs611097

Variant names:

• chr7-64298295-G-A
• rs611097
• ENST00000752314.1:n.197C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-64298295-G-A
• chr7-64298295-G-C
• chr7-64298295-G-T

Variant summary

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

The ENST00000752314.1(ENSG00000287699):​n.197C>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 0.836 in 152,142 control chromosomes in the GnomAD database, including 55,154 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 0.84 (55154 hom., cov: 32)
• Consequence: ENSG00000287699 ENST00000752314.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.878
• Publications: 1 publications found

Genes affected

ENSG00000287699 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000752314.1. 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
	ENSG00000287699	ENST00000752314.1		n.197C>T		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000287699	ENST00000752316.1		n.197C>T		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000287699	ENST00000657968.2		n.242+83C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127076 AN: 152024 Hom.: 55144 Cov.: 32

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.940

Gnomad AMR AF: 0.924

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.971

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.860

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

GnomAD4 genome AF: 0.836 AC: 127118 AN: 152142 Hom.: 55154 Cov.: 32 AF XY: 0.839 AC XY: 62389 AN XY: 74372

African (AFR) AF: 0.572 AC: 23714 AN: 41440

American (AMR) AF: 0.924 AC: 14139 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3063 AN: 3472

East Asian (EAS) AF: 0.905 AC: 4678 AN: 5170

South Asian (SAS) AF: 0.889 AC: 4292 AN: 4830

European-Finnish (FIN) AF: 0.971 AC: 10277 AN: 10584

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.941 AC: 64009 AN: 68032

Other (OTH) AF: 0.861 AC: 1820 AN: 2114

Alfa AF: 0.880 Hom.: 19629

Bravo AF: 0.821

Asia WGS AF: 0.868 AC: 3017 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.19
PhyloP100		-0.88

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: rs611097;

hg19: chr7-63758673;