rs9449067

Variant names:

• chr6-80555778-C-A
• rs9449067

Your query was ambiguous. Multiple possible variants found:

• chr6-80555778-C-A
• chr6-80555778-C-G
• chr6-80555778-C-T

Variant summary

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

The variant allele was found at a frequency of 0.618 in 217,572 control chromosomes in the GnomAD database, including 43,059 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 0.63 (31650 hom., cov: 31)
  • Exomes 𝑓: 0.58 (11409 hom.)
• Consequence: LOC648934 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412
• Publications: 4 publications found

Genes affected

LOC648934 (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 = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC648934		n.80555778C>A		intragenic_variant
LOC112267962	XR_002956360.2	n.91-24535C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000216352	ENST00000403828.1	n.*63G>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.632 AC: 95957 AN: 151768 Hom.: 31599 Cov.: 31

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.635

GnomAD4 exome AF: 0.584 AC: 38376 AN: 65684 Hom.: 11409 AF XY: 0.583 AC XY: 21778 AN XY: 37374

African (AFR) AF: 0.848 AC: 1533 AN: 1808

American (AMR) AF: 0.685 AC: 5083 AN: 7422

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 542 AN: 836

East Asian (EAS) AF: 0.665 AC: 2500 AN: 3762

South Asian (SAS) AF: 0.721 AC: 4387 AN: 6088

European-Finnish (FIN) AF: 0.486 AC: 7026 AN: 14442

Middle Eastern (MID) AF: 0.628 AC: 54 AN: 86

European-Non Finnish (NFE) AF: 0.552 AC: 16000 AN: 29006

Other (OTH) AF: 0.560 AC: 1251 AN: 2234

GnomAD4 genome AF: 0.632 AC: 96068 AN: 151888 Hom.: 31650 Cov.: 31 AF XY: 0.632 AC XY: 46875 AN XY: 74216

African (AFR) AF: 0.829 AC: 34336 AN: 41426

American (AMR) AF: 0.632 AC: 9632 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2197 AN: 3468

East Asian (EAS) AF: 0.671 AC: 3461 AN: 5156

South Asian (SAS) AF: 0.713 AC: 3429 AN: 4808

European-Finnish (FIN) AF: 0.461 AC: 4850 AN: 10532

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36222 AN: 67934

Other (OTH) AF: 0.632 AC: 1333 AN: 2108

Alfa AF: 0.509 Hom.: 2449

Bravo AF: 0.651

Asia WGS AF: 0.700 AC: 2434 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.4
DANN	Benign	0.45
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs9449067; hg19: chr6-81265495; COSMIC: COSV67908945;