rs7665590

Variant names:

• chr4-98875633-T-C
• rs7665590

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 0.559 in 151,368 control chromosomes in the GnomAD database, including 26,076 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 0.56 (26076 hom., cov: 30)
  • Exomes 𝑓: 0.28 (6 hom.)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84490 AN: 151248 Hom.: 26012 Cov.: 30

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.552

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.277 AC: 26 AN: 94 Hom.: 6 Cov.: 0 AF XY: 0.256 AC XY: 20 AN XY: 78

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.256 AC: 21 AN: 82

Other (OTH) AF: 0.750 AC: 3 AN: 4

GnomAD4 genome AF: 0.559 AC: 84622 AN: 151368 Hom.: 26076 Cov.: 30 AF XY: 0.555 AC XY: 41029 AN XY: 73924

African (AFR) AF: 0.836 AC: 34485 AN: 41266

American (AMR) AF: 0.503 AC: 7651 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1732 AN: 3460

East Asian (EAS) AF: 0.681 AC: 3436 AN: 5046

South Asian (SAS) AF: 0.397 AC: 1913 AN: 4814

European-Finnish (FIN) AF: 0.447 AC: 4691 AN: 10496

Middle Eastern (MID) AF: 0.426 AC: 121 AN: 284

European-Non Finnish (NFE) AF: 0.429 AC: 29093 AN: 67776

Other (OTH) AF: 0.552 AC: 1156 AN: 2096

Alfa AF: 0.293 Hom.: 2584

Bravo AF: 0.581

Asia WGS AF: 0.525 AC: 1831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.11
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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: rs7665590;

hg19: chr4-99796784;