rs3740621

Positions:

• chr11-1750567-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001170820.4(IFITM10):​c.-125A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 1,243,332 control chromosomes in the GnomAD database, including 45,360 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 0.32 (9710 hom., cov: 31)
  • Exomes 𝑓: 0.25 (35650 hom.)
• Consequence: IFITM10 NM_001170820.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15

Genes affected

IFITM10 (HGNC:40022): (interferon induced transmembrane protein 10) Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000250644 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IFITM10	NM_001170820.4	c.-125A>G		5_prime_UTR_variant	1/3	ENST00000340134.5	NP_001164291.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFITM10	ENST00000340134.5	c.-125A>G		5_prime_UTR_variant	1/3	3	NM_001170820.4	ENSP00000344430.4
ENSG00000250644	ENST00000636615.1	c.1072-2448A>G		intron_variant		5		ENSP00000490014.1

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49074 AN: 151786 Hom.: 9685 Cov.: 31

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.318

GnomAD4 exome AF: 0.247 AC: 269392 AN: 1091430 Hom.: 35650 Cov.: 15 AF XY: 0.246 AC XY: 133629 AN XY: 543890

Gnomad4 AFR exome AF: 0.567

Gnomad4 AMR exome AF: 0.221

Gnomad4 ASJ exome AF: 0.330

Gnomad4 EAS exome AF: 0.215

Gnomad4 SAS exome AF: 0.233

Gnomad4 FIN exome AF: 0.165

Gnomad4 NFE exome AF: 0.240

Gnomad4 OTH exome AF: 0.271

GnomAD4 genome AF: 0.324 AC: 49156 AN: 151902 Hom.: 9710 Cov.: 31 AF XY: 0.316 AC XY: 23437 AN XY: 74252

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.318

Alfa AF: 0.259 Hom.: 6933

Bravo AF: 0.341

Asia WGS AF: 0.248 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.28
DANN	Benign	0.45
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		0.99

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

Publications

LitVar

Other links and lift over

dbSNP: rs3740621; hg19: chr11-1771797;