rs1011170

Variant names:

• chr6-90620491-A-C
• rs1011170
• ENST00000806370.1:n.146+9954A>C

Your query was ambiguous. Multiple possible variants found:

• chr6-90620491-A-C
• chr6-90620491-A-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000806370.1(ENSG00000304803):​n.146+9954A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,040 control chromosomes in the GnomAD database, including 8,049 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 0.31 (8049 hom., cov: 32)
• Consequence: ENSG00000304803 ENST00000806370.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170
• Publications: 2 publications found

Genes affected

ENSG00000304803 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000806370.1. 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
	ENSG00000304803	ENST00000806370.1		n.146+9954A>C		intron	N/A
	ENSG00000304803	ENST00000806371.1		n.119+6939A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47517 AN: 151922 Hom.: 8042 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.313 AC: 47554 AN: 152040 Hom.: 8049 Cov.: 32 AF XY: 0.318 AC XY: 23655 AN XY: 74330

African (AFR) AF: 0.267 AC: 11094 AN: 41474

American (AMR) AF: 0.342 AC: 5219 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1351 AN: 3460

East Asian (EAS) AF: 0.733 AC: 3792 AN: 5174

South Asian (SAS) AF: 0.464 AC: 2241 AN: 4826

European-Finnish (FIN) AF: 0.325 AC: 3436 AN: 10568

Middle Eastern (MID) AF: 0.377 AC: 110 AN: 292

European-Non Finnish (NFE) AF: 0.285 AC: 19380 AN: 67948

Other (OTH) AF: 0.339 AC: 716 AN: 2110

Alfa AF: 0.294 Hom.: 1176

Bravo AF: 0.315

Asia WGS AF: 0.516 AC: 1794 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	11
DANN	Benign	0.85
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs1011170; hg19: chr6-91330210; COSMIC: COSV69412537;