rs1476442

Variant names:

• chr7-91643029-A-C
• rs1476442
• ENST00000415249.2:n.139+345T>G

Your query was ambiguous. Multiple possible variants found:

• chr7-91643029-A-C
• chr7-91643029-A-G
• chr7-91643029-A-T

Variant summary

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

The ENST00000415249.2(ENSG00000223665):​n.139+345T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,108 control chromosomes in the GnomAD database, including 5,543 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 0.24 (5543 hom., cov: 32)
• Consequence: ENSG00000223665 ENST00000415249.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.80
• Publications: 6 publications found

Genes affected

ENSG00000223665 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000415249.2. 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
	ENSG00000223665	ENST00000415249.2	TSL:4	n.139+345T>G		intron	N/A
	ENSG00000223665	ENST00000718159.1		n.97+345T>G		intron	N/A
	ENSG00000223665	ENST00000718160.1		n.215+345T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35870 AN: 151990 Hom.: 5521 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.236 AC: 35935 AN: 152108 Hom.: 5543 Cov.: 32 AF XY: 0.230 AC XY: 17073 AN XY: 74376

African (AFR) AF: 0.445 AC: 18464 AN: 41458

American (AMR) AF: 0.190 AC: 2906 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 527 AN: 3470

East Asian (EAS) AF: 0.131 AC: 680 AN: 5182

South Asian (SAS) AF: 0.131 AC: 632 AN: 4828

European-Finnish (FIN) AF: 0.119 AC: 1261 AN: 10600

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.160 AC: 10872 AN: 67968

Other (OTH) AF: 0.204 AC: 431 AN: 2108

Alfa AF: 0.199 Hom.: 6515

Bravo AF: 0.252

Asia WGS AF: 0.156 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.2
DANN	Benign	0.55
PhyloP100		1.8
Mutation Taster		=100/0	polymorphism

Splicing

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: rs1476442;

hg19: chr7-91272344;