rs7849955

Variant names:

• chr9-117803051-G-A
• rs7849955
• ENST00000697666.1:c.141-45014G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-117803051-G-A
• chr9-117803051-G-T

Variant summary

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

The ENST00000697666.1(ENSG00000285082):​c.141-45014G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,044 control chromosomes in the GnomAD database, including 1,590 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 0.14 (1588 hom., cov: 32)
  • Exomes 𝑓: 0.075 (2 hom.)
• Consequence: ENSG00000285082 ENST00000697666.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 2 publications found

Genes affected

ENSG00000285082 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376244	XR_007061905.1	n.2899G>A		non_coding_transcript_exon_variant	Exon 7 of 8
LOC105376244	XR_007061906.1	n.2316G>A		non_coding_transcript_exon_variant	Exon 8 of 9
LOC105376244	XR_007061907.1	n.2146+35801G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285082	ENST00000697666.1	c.141-45014G>A		intron_variant	Intron 3 of 4			ENSP00000513391.1

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20650 AN: 151820 Hom.: 1587 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.00233

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0749

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.151

GnomAD4 exome AF: 0.0755 AC: 8 AN: 106 Hom.: 2 Cov.: 0 AF XY: 0.0625 AC XY: 4 AN XY: 64

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0641 AC: 5 AN: 78

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.107 AC: 3 AN: 28

Other (OTH) AC: 0 AN: 0

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.001340), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.136 AC: 20662 AN: 151938 Hom.: 1588 Cov.: 32 AF XY: 0.131 AC XY: 9705 AN XY: 74276

African (AFR) AF: 0.114 AC: 4722 AN: 41482

American (AMR) AF: 0.144 AC: 2189 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 893 AN: 3466

East Asian (EAS) AF: 0.00233 AC: 12 AN: 5146

South Asian (SAS) AF: 0.109 AC: 525 AN: 4824

European-Finnish (FIN) AF: 0.0749 AC: 794 AN: 10606

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11125 AN: 67878

Other (OTH) AF: 0.151 AC: 318 AN: 2108

Alfa AF: 0.140 Hom.: 907

Bravo AF: 0.138

Asia WGS AF: 0.0620 AC: 217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.58
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7849955; hg19: chr9-120565329; COSMIC: COSV101414410;