rs6971109

Variant names:

• chr7-21183171-C-T
• rs6971109
• ENST00000842806.1:n.172+9493C>T

Variant summary

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

The ENST00000842806.1(ENSG00000309656):​n.172+9493C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 151,750 control chromosomes in the GnomAD database, including 5,564 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 0.26 (5564 hom., cov: 32)
• Consequence: ENSG00000309656 ENST00000842806.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 3 publications found

Genes affected

ENSG00000309656 (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 (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000842806.1. 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
	ENSG00000309656	ENST00000842806.1		n.172+9493C>T		intron	N/A
	ENSG00000309656	ENST00000842807.1		n.159+9493C>T		intron	N/A
	ENSG00000309656	ENST00000842808.1		n.550-1958C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39214 AN: 151632 Hom.: 5552 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.259 AC: 39264 AN: 151750 Hom.: 5564 Cov.: 32 AF XY: 0.254 AC XY: 18844 AN XY: 74134

African (AFR) AF: 0.386 AC: 15961 AN: 41338

American (AMR) AF: 0.192 AC: 2933 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 911 AN: 3470

East Asian (EAS) AF: 0.209 AC: 1080 AN: 5162

South Asian (SAS) AF: 0.232 AC: 1116 AN: 4818

European-Finnish (FIN) AF: 0.196 AC: 2055 AN: 10478

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.214 AC: 14514 AN: 67932

Other (OTH) AF: 0.246 AC: 517 AN: 2098

Alfa AF: 0.232 Hom.: 11576

Bravo AF: 0.263

Asia WGS AF: 0.243 AC: 847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.50
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs6971109; hg19: chr7-21222790;